chr6:100868779:G>T Detail (hg19) (SIM1, SIM1-AS1)

Information

Genome

Assembly Position
hg19 chr6:100,868,779-100,868,779
hg38 chr6:100,420,903-100,420,903 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_005068.2:c.1054C>A NP_005059.2:p.Pro352Thr
Ensemble ENST00000262901.4:c.1054C>A ENST00000262901.4:p.Pro352Thr
ENST00000369208.8:c.1054C>A ENST00000369208.8:p.Pro352Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.447
ToMMo:0.484
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.427

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 603128 OMIM
HGNC 10882 HGNC
Ensembl ENSG00000112246 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv26384641 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-01-13 criteria provided, single submitter Obesity due to SIM1 deficiency germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 obesity A nominal evidence of association was found for the nonsynonymous variant P352T ... BeFree 20075856 Detail
<0.001 Language Disorders Firstly, we found a statistically significant association between the SIM1 SNP r... BeFree 24635660 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005068.3(SIM1):c.1054C>A (p.Pro352Thr) AND Obesity due to SIM1 deficiency ClinVar Detail
NM_005068.3(SIM1):c.1054C>A (p.Pro352Thr) AND not provided ClinVar Detail
A nominal evidence of association was found for the nonsynonymous variant P352T C/A (rs3734354) (P =... DisGeNET Detail
Firstly, we found a statistically significant association between the SIM1 SNP rs3734354 (Pro352Thr)... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs3734354 dbSNP
Genome
hg19
Position
chr6:100,868,779-100,868,779
Variant Type
snv
Reference Allele
G
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
979
Mean of sample read depth (HGVD)
36.07
Standard deviation of sample read depth (HGVD)
13.84
Number of reference allele (HGVD)
1081
Number of alternative allele (HGVD)
875
Allele Frequency (HGVD)
0.44734151329243355
Gene Symbol (HGVD)
SIM1
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs3734354
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4838
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8108
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8546
East Asian Allele Counts (ExAC)
3650
East Asian Heterozygous Counts (ExAC)
2150
East Asian Homozygous Counts (ExAC)
750
East Asian Allele Frequency (ExAC)
0.4271003978469459
Chromosome Counts in All Race (ExAC)
119888
Allele Counts in All Race (ExAC)
20717
Heterozygous Counts in All Race (ExAC)
16199
Homozygous Counts in All Race (ExAC)
2258
Allele Frequency in All Race (ExAC)
0.17280294941945817
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